SOLVENT INFLUENCE ON PROTEIN DYNAMICS

The influence of solvent viscosity on the dynamics of small biopolymers, like the alanine dipeptide, is clearly illustrated by the results given here. However, it is necessary to determine whether for larger biopolymers like globular proteins, the solvent influence on the dynamics can also be related to the viscosity alone. Below we provide evidence to the contrary. It is found that the solvent does not affect all atoms and all of their dynamical properties in the same way. Thus, a description based on only the solvent viscosity is not adequate, even disregarding possible alterations in the potential of mean force. 

Proteins do not work in isolation, and it goes without saying that the solvent environment plays an important role in processes involving energy flow in proteins. In addition to comprising a major contribution to the relative thermodynamic stability of different protein conformations, the solvent environment has a major influence on protein dynamics. Indeed, the concept of slaving has been invoked to discuss the control of protein motion by bulk solvent dynamical properties, such as viscosity and dielectric relaxation rates [2,4],... 

In this volume not all stress types are treated. Various aspects have been reviewed recently by various authors e.g. The effects of oxygen on recombinant protein expression by Konz et al. [2]. The Mechanisms by which bacterial cells respond to pH was considered in a Symposium in 1999 [3] and solvent effects were reviewed by de Bont in the article Solvent-tolerant bacteria in biocatalysis [4]. Therefore, these aspects are not considered in this volume. Influence of fluid dynamical stresses on micro-organism, animal and plant cells are in center of interest in this volume. In chapter 2, H.-J. Henzler discusses the quantitative evaluation of fluid dynamical stresses in various type of reactors with different methods based on investigations performed on laboratory an pilot plant scales. S. S. Yim and A. Shamlou give a general review on the effects of fluid dynamical and mechanical stresses on micro-organisms and bio-polymers in chapter 3. G. Ketzmer describes the effects of shear stress on adherent cells in chapter 4. Finally, in chapter 5, P. Kieran considers the influence of stress on plant cells. 

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins.38 The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions.39 Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent.40 A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions 41,42 Molecular and chiral recognition rely on... 

Because of the ease with which molecular mechanics calculations may be obtained, there was early recognition that inclusion of solvation effects, particularly for biological molecules associated with water, was essential to describe experimentally observed structures and phenomena [32]. The solvent, usually an aqueous phase, has a fundamental influence on the structure, thermodynamics, and dynamics of proteins at both a global and local level [3/]. Inclusion of solvent effects in a simulation of bovine pancreatic trypsin inhibitor produced a time-averaged structure much more like that observed in high-resolution X-ray studies with smaller atomic amplitudes of vibration and a fewer number of incorrect hydrogen bonds [33], High-resolution proton NMR studies of protein hydration in aqueous... 

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